moleculekit.projections.metricrmsd module

class moleculekit.projections.metricrmsd.MetricRmsd(refmol, trajrmsdstr, trajalnstr=None, refrmsdstr=None, refalnstr=None, centerstr='protein', pbc=True)

Bases: moleculekit.projections.projection.Projection

Calculates the RMSD of a set of trajectories to a reference structure

Parameters

  • refmol (Molecule object) – The reference Molecule to which we want to calculate the RMSD.

  • trajrmsdstr (str) – Atom selection string for the trajectories from which to calculate the RMSD. See more here

  • trajalnstr (str, optional) – Atom selection string for the trajectories from which to align to the reference structure. If None, it defaults to the same as trajrmsdstr. See more here

  • refrmsdstr (str, optional) – Atom selection string for the reference structure from which to calculate the RMSD. If None, it defaults to trajrmsdstr. See more here

  • refalnstr (str, optional) – Atom selection string for the reference structure from which to align to the trajectories. If None, it defaults to trajalnstr. See more here

  • centerstr (str, optional) – Atom selection string around which to center the wrapping of the trajectories. See more here

  • pbc (bool, optional) – Enable or disable simulation wrapping.

getMapping(mol)

Returns the description of each projected dimension.

Parameters

mol (Molecule object) – A Molecule object which will be used to calculate the descriptions of the projected dimensions.

Returns

map – A DataFrame containing the descriptions of each dimension

Return type

DataFrame object

project(mol)

Project molecule.

Parameters

mol (Molecule) – A Molecule object to project.

Returns

data – An array containing the projected data.

Return type

np.ndarray